Contacts of the helix formed by residues 123 - 149 (chain B) in PDB entry 4TVQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU 2.9 9.2 + - - +
121B ILE 3.2 1.7 - - - -
122B ASN* 1.3 81.5 - - - +
124B ARG* 1.3 60.2 + - - +
125B VAL* 3.2 12.8 + - - +
126B ARG* 2.8 70.6 + - - +
127B PHE* 2.8 29.9 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE 5.1 0.4 + - - -
122B ASN 4.3 0.4 - - - -
123B ASP* 1.3 72.4 - - - +
125B VAL* 1.3 60.0 + - + +
127B PHE* 3.8 7.4 - - - +
128B LEU* 2.9 32.7 + - - +
182B PHE* 6.4 2.0 - - + -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 3.2 9.7 + - - +
124B ARG* 1.3 75.4 - - + +
126B ARG* 1.3 68.7 + - + +
128B LEU* 3.1 8.2 + - - +
129B GLN* 2.9 49.9 + - + +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASP* 2.7 30.5 + - - +
120B GLU* 3.2 25.9 + - + +
122B ASN* 5.6 2.8 - - - +
123B ASP* 2.8 46.0 + - - +
125B VAL* 1.3 75.0 - - + +
127B PHE* 1.3 52.8 + - - +
129B GLN* 3.5 16.7 + - - +
130B THR* 2.6 37.7 + - - -
108D ARG* 5.4 8.3 - - - +
112D GLN* 5.1 10.4 - - - +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 4.2 19.5 - - + -
120B GLU* 3.2 10.2 + - + +
121B ILE* 3.6 44.6 - - + +
123B ASP 2.8 21.1 + - - +
124B ARG* 3.8 6.5 - - - +
126B ARG* 1.3 77.0 - - - +
128B LEU* 1.3 58.0 + - + +
130B THR* 3.2 13.2 + - + -
131B ILE* 2.9 53.6 + - + +
134B ILE* 6.3 1.1 - - + -
174B PHE* 6.2 0.2 - + - -
178B LEU* 3.7 24.9 - - + -
181B TYR* 3.9 20.2 - + - -
182B PHE* 3.9 21.8 - + - -
190B VAL* 4.6 2.5 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG 2.9 19.7 + - - +
125B VAL* 3.1 7.2 + - - +
127B PHE* 1.3 73.6 - - - +
129B GLN* 1.3 60.0 + - + +
131B ILE* 3.1 26.1 + - + +
132B LYS* 2.9 36.0 + - + +
182B PHE* 4.7 11.7 - - + -
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 2.9 35.0 + - + +
126B ARG* 3.7 19.3 - - - +
128B LEU* 1.3 76.9 - - + +
130B THR* 1.3 57.3 + - - +
132B LYS* 3.1 20.4 + - + +
133B ASP* 3.0 36.6 + - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.3 21.0 - - + +
116B LYS* 5.3 0.7 - - + +
117B ILE* 4.5 11.2 - - + -
120B GLU* 3.3 27.3 - - + +
126B ARG 2.6 20.7 + - - -
127B PHE* 3.3 15.9 - - + -
129B GLN* 1.3 77.6 - - - +
131B ILE* 1.3 56.7 + - - +
133B ASP* 3.3 8.5 + - - +
134B ILE* 2.9 52.8 + - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PHE* 2.9 53.2 + - + +
128B LEU* 3.1 21.3 + - + +
130B THR* 1.3 73.4 - - - +
132B LYS* 1.3 59.9 + - - +
134B ILE* 3.5 10.4 + - + +
135B ALA* 2.9 31.1 + - + +
174B PHE* 6.1 1.1 - - + -
178B LEU* 4.2 26.7 - - + -
182B PHE* 3.7 20.6 - - + -
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 2.9 19.8 + - + +
129B GLN* 3.2 25.4 - - + +
131B ILE* 1.3 76.0 - - - +
133B ASP* 1.3 66.9 + - - +
135B ALA* 3.1 9.1 + - - +
136B SER* 2.9 23.0 + - - -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE* 4.2 23.5 - - + +
129B GLN* 3.0 26.5 + - - +
130B THR* 3.7 6.6 - - - +
132B LYS* 1.3 77.9 - - - +
134B ILE* 1.3 57.5 + - - +
136B SER* 3.3 8.4 + - - -
137B ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 4.4 2.5 - - + -
113B ILE* 3.8 24.7 - - + +
114B LEU* 3.7 29.2 - - + -
117B ILE* 3.8 19.1 - - + -
127B PHE* 6.3 0.9 - - + -
130B THR* 2.9 34.5 + - + +
131B ILE* 3.8 9.4 - - + +
133B ASP* 1.3 73.1 - - - +
135B ALA* 1.3 61.1 + - - +
137B ALA* 3.2 6.6 + - - +
138B ILE* 2.9 49.7 + - + +
174B PHE* 4.3 17.0 - - + -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 2.9 18.1 + - + +
132B LYS* 3.3 11.2 - - - +
134B ILE* 1.3 78.2 - - - +
136B SER* 1.3 57.2 + - - +
138B ILE* 3.8 8.6 - - - +
139B LYS* 2.9 30.0 + - - +
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LYS 2.9 12.3 + - - -
133B ASP* 3.5 12.1 - - - -
135B ALA* 1.3 77.2 - - - +
137B ALA* 1.3 57.2 + - - +
139B LYS* 3.4 7.8 + - - +
140B GLU* 2.9 46.6 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 5.0 3.6 - - - +
109B ALA* 4.9 5.2 - - + -
110B LEU* 3.7 36.0 - - + +
113B ILE* 4.4 5.6 - - + -
133B ASP 2.9 17.2 + - - +
134B ILE* 3.2 6.9 + - - +
136B SER* 1.3 77.1 - - - +
138B ILE* 1.3 56.9 + - - +
140B GLU* 3.5 8.4 + - - +
141B LEU* 2.9 31.4 + - - +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 3.7 24.2 - - + -
134B ILE* 2.9 37.0 + - + +
135B ALA* 3.8 7.0 - - - +
137B ALA* 1.3 73.4 - - - +
139B LYS* 1.3 59.6 + - - +
141B LEU* 3.5 2.7 + - - +
142B LEU* 2.9 33.6 + - + +
167B PHE* 3.8 18.5 - - + -
171B SER* 3.6 28.5 - - - +
174B PHE* 5.1 6.7 - - + -
197B LEU* 4.0 17.3 - - + -
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ALA 2.9 16.6 + - - +
136B SER* 3.7 7.4 - - - +
138B ILE* 1.3 78.4 - - - +
140B GLU* 1.3 59.0 + - + +
142B LEU* 3.2 12.1 + - + +
143B ASP* 2.9 47.5 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 3.5 33.1 - - + +
136B SER* 2.9 30.8 + - - +
137B ALA* 3.9 6.7 - - - +
139B LYS* 1.3 75.3 - - + +
141B LEU* 1.3 56.8 + - - +
143B ASP* 3.3 11.2 + - - +
144B THR* 2.6 37.0 + - - -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.1 23.6 - - + +
106B LYS* 3.7 27.9 - - + +
107B ALA* 4.0 14.1 - - + +
110B LEU* 3.6 26.9 - - + -
137B ALA 2.9 18.3 + - - +
138B ILE* 3.9 4.7 - - - +
140B GLU* 1.3 75.7 - - - +
142B LEU* 1.3 57.5 + - - +
144B THR* 3.4 1.3 + - - -
145B VAL* 2.9 42.8 + - + +
167B PHE* 3.7 20.4 - - + -
201B THR* 4.3 15.5 - - + -
204B ILE* 6.0 2.2 - - + -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ILE* 2.9 20.3 + - + +
139B LYS* 3.2 15.0 - - + +
141B LEU* 1.3 77.4 - - - +
143B ASP* 1.3 68.4 + - - +
145B VAL* 3.2 8.7 + - - +
146B ASN* 2.9 51.8 + - - +
164B LYS* 5.4 8.5 - - - -
167B PHE* 5.3 9.6 - - + -
168B VAL* 4.7 19.7 - - + -
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Residues in contact with ASP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LYS* 2.9 36.5 + - - +
140B GLU* 3.3 11.5 + - - +
142B LEU* 1.3 89.4 - - - +
144B THR* 1.3 53.4 + - - +
146B ASN* 3.2 13.4 + - - +
147B ASN* 2.5 41.3 + - - +
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 4.2 4.0 - - - +
102B ASP* 3.8 13.1 - - + +
103B LEU* 3.5 43.3 - - + +
106B LYS* 3.3 21.6 + - - +
140B GLU 2.6 22.9 + - - -
141B LEU* 3.7 5.4 - - - -
143B ASP* 1.3 72.8 - - - +
145B VAL* 1.3 61.5 + - - +
147B ASN* 3.0 15.3 + - + +
148B VAL* 2.9 32.0 + - + +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.4 4.0 - - + -
141B LEU* 2.9 36.2 + - + +
142B LEU* 3.4 8.5 - - - +
144B THR* 1.3 75.4 - - - +
146B ASN* 1.3 59.4 + - - +
148B VAL* 3.3 9.8 + - - +
149B PHE* 3.0 28.5 + - + +
164B LYS* 4.6 30.1 - - + -
167B PHE* 6.2 3.4 - - + -
204B ILE* 5.0 12.1 - - + -
208B PHE* 4.3 24.1 - - + -
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Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 2.9 41.6 + - - +
143B ASP* 3.3 14.7 + - - +
145B VAL* 1.3 79.2 - - - +
147B ASN* 1.3 60.1 + - - +
149B PHE* 3.6 22.6 + - - +
164B LYS* 3.0 33.5 + - - +
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Residues in contact with ASN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 4.2 28.4 - - + +
143B ASP* 2.5 38.2 + - - +
144B THR* 3.0 15.8 + - + +
146B ASN* 1.3 76.7 - - - +
148B VAL* 1.3 65.4 + - - +
149B PHE 3.3 4.7 + - - -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 4.5 16.8 - - + +
100B PHE* 4.5 19.3 - - + -
103B LEU* 3.7 33.9 - - + -
144B THR* 2.9 20.1 + - + +
145B VAL* 3.7 6.7 - - - +
147B ASN* 1.3 77.1 - - - +
149B PHE* 1.3 64.8 + - - +
208B PHE* 3.8 31.0 - - + -
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 3.0 18.3 + - + +
146B ASN* 3.7 17.5 - - - +
147B ASN 3.2 5.1 - - - -
148B VAL* 1.3 82.7 - - - +
161B GLU* 3.2 39.3 - - + -
164B LYS* 6.4 0.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il